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Load a database with biopython objects.
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Initialize with connection information for the database. XXX Figure out what I need to load a database and document it. |
Returns the identifier for the named ontology. This looks through the onotology table for a the given entry name. If it is not found, a row is added for this ontology (using the definition if supplied). In either case, the id corresponding to the provided name is returned, so that you can reference it in another table. |
Get the id that corresponds to a term. This looks through the term table for a the given term. If it is not found, a new id corresponding to this term is created. In either case, the id corresponding to that term is returned, so that you can reference it in another table. The ontology_id should be used to disambiguate the term. |
Get the taxon id for this record. record - a SeqRecord object This searches the taxon/taxon_name tables using the NCBI taxon ID, scientific name and common name to find the matching taxon table entry's id. If the species isn't in the taxon table, and we have at least the NCBI taxon ID, scientific name or common name, a minimal stub entry is created in the table. If this information is not in the record's annotation, then None is returned. See also the BioSQL script load_ncbi_taxonomy.pl which will populate and update the taxon/taxon_name tables with the latest information from the NCBI. |
Fill the bioentry table with sequence information. record - SeqRecord object to add to the database. |
Add the effective date of the entry into the database. record - a SeqRecord object with an annotated date bioentry_id - corresponding database identifier |
Record a SeqRecord's sequence and alphabet in the database. record - a SeqRecord object with a seq property bioentry_id - corresponding database identifier |
Record a SeqRecord's annotated comment in the database. record - a SeqRecord object with an annotated comment bioentry_id - corresponding database identifier |
Record a SeqRecord's misc annotations in the database. The annotation strings are recorded in the bioentry_qualifier_value table, except for special cases like the reference, comment and taxonomy which are handled with their own tables. record - a SeqRecord object with an annotations dictionary bioentry_id - corresponding database identifier |
Record a SeqRecord's annotated references in the database. record - a SeqRecord object with annotated references bioentry_id - corresponding database identifier |
Load the first tables of a seqfeature and returns the id. This loads the "key" of the seqfeature (ie. CDS, gene) and the basic seqfeature table itself. |
Load all of the locations for a SeqFeature into tables. This adds the locations related to the SeqFeature into the seqfeature_location table. Fuzzies are not handled right now. For a simple location, ie (1..2), we have a single table row with seq_start = 1, seq_end = 2, location_rank = 1. For split locations, ie (1..2, 3..4, 5..6) we would have three row tables with: start = 1, end = 2, rank = 1 start = 3, end = 4, rank = 2 start = 5, end = 6, rank = 3 |
Insert the (key, value) pair qualifiers relating to a feature. Qualifiers should be a dictionary of the form: {key : [value1, value2]} |
Add the database crossreferences of a SeqFeature to the database. o dbxrefs List, dbxref data from the source file in the format <database>:<accession> o seqfeature_id Int, the identifier for the seqfeature in the seqfeature table Insert dbxref qualifier data for a seqfeature into the seqfeature_dbxref and, if required, dbxref tables. The dbxref_id qualifier/value sets go into the dbxref table as dbname, accession, version tuples, with dbxref.dbxref_id being automatically assigned, and into the seqfeature_dbxref table as seqfeature_id, dbxref_id, and rank tuples |
o db String, the name of the external database containing the accession number o accession String, the accession of the dbxref data Finds and returns the dbxref_id for the passed data. The method attempts to find an existing record first, and inserts the data if there is no record.
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Check for a pre-existing seqfeature_dbxref entry with the passed seqfeature_id and dbxref_id. If one does not exist, insert new data |
Load any sequence level cross references into the database. See table bioentry_dbxref |
Check for a pre-existing bioentry_dbxref entry with the passed seqfeature_id and dbxref_id. If one does not exist, insert new data |
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